Take a deep breath and relax.
Sometimes all you need is a tune up. Just like maintenance on your car, your roof needs a tune up every once in a while. If your home still has the roof the builder put on, chances are the fine details were not covered. It was completely covered with shingles and all of the accessories, but they did not take the time to caulk all the exposed nails, check all the underdriven nails, caulk the seams at intersecting ridge caps, etc. With weathering and time, the nails rust, the "nail pops" burst through the overlapping shingle, and the gaps at the uncaulked seams give way to rain. The best and most cost effective solution is a roof tune up. It's worth saving thousands to extend the life of your roof. You wouldn't buy a new car when you need an oil change or new tires, right?
Even homes that are older can experience these problems. What's the warranty on caulking? NOT 25 years!! I've seen nails in vents standing right over their holes with caulking still on the nail heads. Water enters through the uncovered nail hole and... you know the rest. So if you feel that your roof is failing a bit too soon for its age, don't jump to conclusions